I'm quality-checking the mouse ChIP-seq data with ChIPQC, but for some reason the coverage plot behaves weirdly. After this, I ran the samples by chromosomes and found out it is chr Y - which has much less reads than others - which is causing the trouble. To demonstrate, here are coverage plots with all the chromosomes, with all but chr Y, and with chr Y only.

However, it may have something to do with how chromosomes are combined: I took two non-problematic chromosomes, and started to down-sample the other one, and ran ChIPQC for the combined file. Some "cracks" do appear, though not as drastic as in the figures I linked before. I assume that the coverage plots should approach that of the intact chromosome when inputting less and less reads from the other chromosome.